This is why I like to put my support ships in different control groups.  There isn't a graceful way to get around the issue, since you either have to have several control groups for each task force of ships, or one big control group that isn't useful for issuing tactical commands in battle.

I will say that alt-click is your friend.

If your opponent is using light frigates, they can scoot past your LRF and start blasting the carriers, forcing them to jump and breaking up your fleet.  If I'm up against an enemy with lots of LF, I keep my carriers close to my LRF so they're covered.  This is doubly true for Advent with shield regeneration and repulsion.